The RNA structurome: transcriptome-wide structure probing with next-generation sequencing

Trends in Biochemical Sciences
Chun Kit KwokPhilip C Bevilacqua

Abstract

RNA folds into intricate structures that enable its pivotal roles in biology, ranging from regulation of gene expression to ligand sensing and enzymatic functions. Therefore, elucidating RNA structure can provide profound insights into living systems. A recent marriage between in vivo RNA structure probing and next-generation sequencing (NGS) has revolutionized the RNA field by enabling transcriptome-wide structure determination in vivo, which has been applied to date to human cells, yeast cells, and Arabidopsis seedlings. Analysis of resultant in vivo 'RNA structuromes' provides new and important information regarding myriad cellular processes, including control of translation, alternative splicing, alternative polyadenylation, energy-dependent unfolding of mRNA, and effects of proteins on RNA structure. An emerging view suggests potential links between RNA structure and stress and disease physiology across the tree of life. As we discuss here, these exciting findings open new frontiers into RNA biology, genome biology, and beyond.

References

May 30, 1978·Biochemistry·T E England, O C Uhlenbeck
Jan 1, 1975·Proceedings of the National Academy of Sciences of the United States of America·G C WalkerR I Gumport
Dec 1, 1986·Proceedings of the National Academy of Sciences of the United States of America·S M FreierD H Turner
Nov 25, 1987·Nucleic Acids Research·C EhresmannB Ehresmann
Oct 1, 1989·Proceedings of the National Academy of Sciences of the United States of America·J A JaegerM Zuker
Jul 20, 2002·Current Opinion in Structural Biology·Robin R GutellJamie J Cannone
May 5, 2004·Proceedings of the National Academy of Sciences of the United States of America·David H MathewsDouglas H Turner
May 5, 2005·Annual Review of Biophysics and Biomolecular Structure·Kenneth F Blount, Olke C Uhlenbeck
Feb 18, 2006·RNA·Neocles B LeontisEric Westhof
May 10, 2006·Nucleic Acids Research·Svetlana A ShabalinaNikolay A Spiridonov
Sep 12, 2007·Nature Reviews. Genetics·Alexander Serganov, Dinshaw J Patel
Dec 26, 2008·Proceedings of the National Academy of Sciences of the United States of America·Katherine E DeiganKevin M Weeks
Feb 26, 2009·Cell·Phillip A Sharp
Mar 17, 2010·BMC Bioinformatics·Jessica S Reuter, David H Mathews
May 8, 2010·Current Opinion in Structural Biology·Kevin M Weeks
Jun 18, 2010·Methods : a Companion to Methods in Enzymology·Justin T Low, Kevin M Weeks
Nov 9, 2010·Nature Methods·Jason G UnderwoodDavid Haussler
Dec 1, 2010·Nature Methods·Eric Westhof, Pascale Romby
Jun 7, 2011·Proceedings of the National Academy of Sciences of the United States of America·Julius B LucksAdam P Arkin
Jun 7, 2011·Proceedings of the National Academy of Sciences of the United States of America·Sharon AviranLior Pachter
Aug 19, 2011·Nature Reviews. Genetics·Yue WanHoward Y Chang
Sep 6, 2011·Nucleic Acids Research·Anitha D JayaprakashRavi Sachidanandam
Apr 12, 2012·Nucleic Acids Research·Fan LiLi-San Wang
Jul 27, 2012·Cell Reports·Fan LiBrian D Gregory
Aug 3, 2012·Journal of the American Chemical Society·Kady-Ann SteenKevin M Weeks
Sep 18, 2012·Molecular Cell·Yue WanHoward Y Chang
Feb 13, 2013·Analytical Biochemistry·Chun Kit KwokPhilip C Bevilacqua
Mar 16, 2013·Nature Protocols·Marie-Theres Gansauge, Matthias Meyer
Mar 19, 2013·Proceedings of the National Academy of Sciences of the United States of America·Christine E HajdinKevin M Weeks
Nov 5, 2013·Methods : a Companion to Methods in Enzymology·Ina HuppertzJernej Ule
Nov 13, 2013·Biochemistry·Jillian TyrrellGary J Pielak

❮ Previous
Next ❯

Citations

Jun 1, 2015·Journal of Molecular Biology·Chelsea M Hull, Philip C Bevilacqua
Aug 25, 2015·Biochimica Et Biophysica Acta·Brian S Gloss, Marcel E Dinger
Nov 26, 2015·Journal of Molecular Biology·Yin TangPhilip C Bevilacqua
Mar 1, 2016·Current Opinion in Structural Biology·Zhipeng Lu, Howard Y Chang
Oct 11, 2015·Biology Direct·Avinash Achar, Pål Sætrom
Nov 7, 2015·Biochemistry·Matthew J SmolaKevin M Weeks
Jun 9, 2016·Quarterly Reviews of Biophysics·Siqi Tian, Rhiju Das
Nov 18, 2015·Nature Chemical Biology·Miles KubotaRobert C Spitale
Apr 12, 2016·Methods : a Companion to Methods in Enzymology·Ronny LorenzIvo L Hofacker
May 2, 2016·Current Opinion in Biotechnology·Eric J StrobelJulius B Lucks
May 20, 2016·International Journal of Molecular Sciences·Rui LiYunbo Luo
Jul 19, 2016·Trends in Biochemical Sciences·Chase A WeidmannKevin M Weeks
Jul 21, 2016·Wiley Interdisciplinary Reviews. RNA·Anne Nitsche, Peter F Stadler
Aug 30, 2016·Nature Methods·Chun Kit KwokShankar Balasubramanian
Nov 8, 2016·Nature Methods·Meghan ZubradtSilvi Rouskin
Dec 19, 2016·Trends in Biotechnology·Danny Incarnato, Salvatore Oliviero
Jan 25, 2017·RNA·Jing ZhangAlastair I H Murchie
Apr 27, 2017·Plant & Cell Physiology·Toshihiro AraeYukako Chiba
Jun 24, 2017·Nucleic Acids Research·Laura E RitcheyPhilip C Bevilacqua
Nov 23, 2017·Nature Reviews. Molecular Cell Biology·Kathrin LeppekMaria Barna
Jun 19, 2019·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Kenneth HodgeSarin Chimnaronk
Dec 3, 2016·Biochemical Society Transactions·Chun Kit Kwok
Sep 19, 2017·Current Protocols in Nucleic Acid Chemistry·Sarah A Woodson
Dec 10, 2019·Current Protocols in Protein Science·Sibel ÖztürkPınar Çalık
Nov 22, 2018·PloS One·Sana VaziriSharon Aviran
Sep 12, 2020·Organic & Biomolecular Chemistry·Saurja DasGupta
Jun 21, 2016·Current Protocols in Bioinformatics·Lars BarquistPaul P Gardner
Sep 16, 2020·Wiley Interdisciplinary Reviews. RNA·Bingbing XuYongfeng Jin
Sep 26, 2020·Nucleic Acids Research·Mubarak I Umar, Chun Kit Kwok
Feb 23, 2019·Genome Biology·Krishna ChoudharySharon Aviran
Jul 3, 2019·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Mubarak I UmarChun Kit Kwok

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.